CSAG1

chondrosarcoma associated gene 1, the group of CSAG family

Basic information

Region (hg38): X:152727484-152733735

Links

ENSG00000198930 ∙ NCBI:158511 ∙ OMIM:300944 ∙ HGNC:24294 ∙ Uniprot:Q6PB30 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSAG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSAG1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			6	1	1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	1

Variants in CSAG1

This is a list of pathogenic ClinVar variants found in the CSAG1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-152727810-G-A		not specified	Uncertain significance (Nov 14, 2023)
X-152727829-C-G		not specified	Uncertain significance (Sep 22, 2023)
X-152727831-G-A		not specified	Uncertain significance (Dec 02, 2022)
X-152728080-G-C			Benign (Apr 03, 2018)
X-152728087-A-G		not specified	Likely benign (Jul 11, 2023)
X-152728101-G-A		not specified	Uncertain significance (May 03, 2023)
X-152728188-C-T		not specified	Uncertain significance (Jun 30, 2023)
X-152728200-A-G		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSAG1	protein_coding	protein_coding	ENST00000370287	3	6291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00361	0.411	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	45	29.2	1.54	0.00000218	488
Missense in Polyphen		24	16.364	1.4666		296
Synonymous	-2.09	21	11.9	1.77	9.54e-7	162
Loss of Function	-0.565	3	2.11	1.42	1.34e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.766
• rvis_EVS: 0.92
• rvis_percentile_EVS: 89.61

Haploinsufficiency Scores

• pHI: 0.0170
• hipred: N
• hipred_score: 0.123
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0852

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium